How can I save the payload of ESP as separate packet after decryption ?

I have the encrypted ESP packets. I am able to decrypt these packets after putting necessary keys and algo inside below filed.
Edit ->Preferences -> ESP

Basically ESP has the inner packet with IP, UDP/TCP, and other user defined protocol..
In my case, I have a separate tool to parse the user defined protocol. But ESP packets does not work in that tool.
The tools works with the wireshark file without ESP.

So can I strip off the IP, UDP and ESP header from the log, so that the log file will be just like as collected before security gateway ?

Not sure that I follow what you are saying. Some meta data from the original file gets saved and interpreted by the "Exported PDU" dissector that meta data "should" contain the next protocol or UDP/TCP port to call as the next dissector. What is displayed after Exported PDU in your trace and what is the protocol following ESP?

No this is what you get, the decrypted data after esp with some metadata from the previous layers saved. Any decoder of this file would have to understand the exported pdu format as wireshark does. The format is documented in the sources.